Evolution of the rapidly mutating human salivary agglutinin gene (DMBT1) and population subsistence strategy

Abstract

The dietary change resulting from the domestication of plant and animal species and development of agriculture at different locations across the world was one of the most significant changes in human evolution. An increase in dietary carbohydrates caused an increase in dental caries following the development of agriculture, mediated by the cariogenic oral bacterium Streptococcus mutans. Salivary agglutinin [SAG, encoded by the deleted in malignant brain tumors 1 (DMBT1) gene] is an innate immune receptor glycoprotein that binds a variety of bacteria and viruses, and mediates attachment of S. mutans to hydroxyapatite on the surface of the tooth. In this study we show that multiallelic copy number variation (CNV) within DMBT1 is extensive across all populations and is predicted to result in between 7-20 scavenger-receptor cysteine-rich (SRCR) domains within each SAG molecule. Direct observation of de novo mutation in multigeneration families suggests these CNVs have a very high mutation rate for a protein-coding locus, with a mutation rate of up to 5% per gamete. Given that the SRCR domains bind S. mutans and hydroxyapatite in the tooth, we investigated the association of sequence diversity at the SAG-binding gene of S. mutans, and DMBT1 CNV. Furthermore, we show that DMBT1 CNV is also associated with a history of agriculture across global populations, suggesting that dietary change as a result of agriculture has shaped the pattern of CNV at DMBT1, and that the DMBT1-S. mutans interaction is a promising model of host-pathogen-culture coevolution in humans.

Keywords: DMBT1; agriculture; copy number variation; mutation; structural variation.

Fig. 1.

Analysis of DMBT1 structure and CNV. (A) Dotplot of the DMBT1 gene (exons and introns) aligned against itself. Lines indicate high similarity and emphasize the repeated nature of the structure of the gene. Individual SRCR domains are indicated and numbered. Note that the canonical DMBT1 gene sequence has one fewer SRCR domain that that predicted by the genome assembly, and the extra SRCR domain is labeled 9’. (B) Exon–intron structure of the DMBT1 gene with CNV signals. Three DMBT1 gene annotations derived from different transcripts are shown. CNV signals from the Database of Genome Variants (dgv.tcag.ca/dgv/app/home) are shown below, with red indicating loss of signal compared with a reference genome, blue gain of signal, and brown both loss and gain of signal observed in different samples. Note that these annotations are often larger than the actual CNV, because they can represent large insert clones that detect a CNV, but with the CNV boundaries unknown. CNV1 and CNV2 are annotated, with the reference genomic sequence showing one copy of the CNV1 region and four copies of the CNV2 region. Figure is based on UCSC Genome Browser screenshot hg19 assembly. (C) Comparison of copy number calling methods for CNV1 (Left) and CNV2 (Right). Each point on the scatterplot represents an individual sample, with different symbols reflecting the final copy number call. The x axes individuate the copy number value estimated from paralog ratio tests (PRTs), and the y axes indicate the first principal component of probe intensity data for probes spanning the CNV in array comparative genomic hybridization (data from ref. 17). (D) Sequence relationship of SRCR repeats. A maximum-likelihood tree shows the relationship of the SRCR repeats (between 3 and 4 kb) carrying the SRCR-coding-domain exon. Scale bar indicates 0.1 substitutions per site. Amino acid sequences of the SRCR domains corresponding to the S. mutans and hydroxyapatite-binding regions are arranged alongside the tree, ordered according to the order of SRCR domains on the tree. Note that the divergent SRCR14 domain does not bind bacteria (54), is not coded by a repeated DNA region (A), and is located at the C-terminal end of the DMBT1^SAG protein.

Fig. 2.

Distribution of DMBT1 copy number values in the CEPH-HGDP panel. (A) Across individuals. Each point represents the mean unrounded PRT copy number of an individual, with the histogram on each axis representing the distribution of CNV1 copy numbers (x axis) and CNV2 copy numbers (y axis). (B) Across populations. The means of CNV1 and CNV2 in each population are plotted, colored according to continent of origin. The red dashed lines represent the value above which 99.5% of mean copy numbers of simulated populations fall. (C) Average CNV1 and CNV2 copy number in agricultural and nonagricultural populations. Populations are colored according to region (legend in B), thick line indicates median value and thin lines are 25th and 75th centiles, and P values from logistic regression, with distance from Africa as a covariate (Table 1). Agricultural population definition is according to ref. .